Manufacturing agglomeration (MA) is an important way to achieve high-quality industrial development and promote land use efficiency in China. However, there is a lack of research on the relationship between MA and the green use efficiency of industrial land (GUEIL). Based on the panel data of 279 prefecture-level cities in China, from 2004 to 2019, this study analyzes the spatial and temporal differentiation characteristics of MA and GUEIL, then empirically analyzes the impact of MA on GUEIL. The results show that: (1) during the study period, the national MA levels showed a slight decline, followed by a small increase. In addition, the inter-regional differences are mainly characterized as eastern region > central region > northeast region > western region. (2) The national and regional GUEIL showed a trend of increasing, slightly decreasing, and then increasing again. The overall regional differences in efficiency show the characteristics of: eastern region > central region > western region > northeastern region. (3) At the national scale, MA had a “U-shaped” relationship with GUEIL; at the regional scale, MA had a significant “U-shaped” effect on GUEIL in the northeast, central and western regions, while having a single negative effect in the eastern region. Finally, this study provides suggestions for optimizing the manufacturing structure and improving the GUEIL.